Characterization of glass micro array

Commonly used quality control of DNA arrays employs hybridization, spotting of labeled DNA, and measurement of the Reflection of salt components left from the spotting buffers. Control hybridizations have the disadvantage that the slides used in the control cannot be reused. Spotting of labeled DNA does not guarantee that all other spots are found on the array. Control by measuring residual salt has the disadvantage that the DNA itself is not detected. By contrast to these methods imaging ellipsometry is the only method that allows the direct control of DNA arrays after the final (washing) step in a label-free and non-destructive manner. The images visualize not a ‘carrier’ component as salt but the DNA itself. Each spot is well resolved and can be judged regarding size, shape, homogeneity, positioning within the array. Imaging ellipsometry allows a quality control of DNA arrays without the need for control hybridizations or control spotting of labeled DNA. It measures thickness, refractive index, and (in case of labeling even) extinction of the spotted reaction layer.

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